Automatic transmissions generate 2-3X more low-end torque so if your idle is even a little high from something like a vacuum leak, I can see this happening.
Or the transmission's kick-down cable might have been adjusted too tight next to the throttle body. It should only be tight enough for the cable to have zero slack in it at idle.
Don't feel like you have a bad choice of transmissions however. Your 3-speed 32RH automatic transmission is one of the best and most bulletproof transmissions to have ever come out of Detroit. Ford even tried to buy the manufacturing rights to it but Chrysler wanted too much $$$ for Ford to agree to it.
I actually converted my last TJ from its OE 5-speed transmission to that very same transmission several years ago. It does much better on extreme-level trails due to its added low-end torque and infinitely low first gear ratio that also provides an infinitely high crawl ratio.